HEADER RNA 11-JAN-11 2L8F TITLE STRUCTURE OF A 4X4 NUCLEOTIDE RNA INTERNAL LOOP FROM AN R2 TITLE 2 RETROTRANSPOSON COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS RNA MOTIF, INTERNAL LOOP, 3RRS, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Y.LERMAN,S.D.KENNEDY,D.H.TURNER REVDAT 1 31-AUG-11 2L8F 0 JRNL AUTH Y.V.LERMAN,S.D.KENNEDY,N.SHANKAR,M.PARISIEN,F.MAJOR, JRNL AUTH 2 D.H.TURNER JRNL TITL NMR STRUCTURE OF A 4 X 4 NUCLEOTIDE RNA INTERNAL LOOP FROM JRNL TITL 2 AN R2 RETROTRANSPOSON: IDENTIFICATION OF A THREE JRNL TITL 3 PURINE-PURINE SHEARED PAIR MOTIF AND COMPARISON TO MC-SYM JRNL TITL 4 PREDICTIONS. JRNL REF RNA V. 17 1664 2011 JRNL REFN ISSN 1355-8382 JRNL PMID 21778280 JRNL DOI 10.1261/RNA.2641911 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON, REMARK 3 SEIBEL,SINGH,WEINER,KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L8F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JAN-11. REMARK 100 THE RCSB ID CODE IS RCSB102086. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 273; 273 REMARK 210 PH : 6.5; 6.5; 5 REMARK 210 IONIC STRENGTH : 0.1; 0.1; 0.1 REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5 MM RNA (5'-R(*GP*UP*GP*AP* REMARK 210 AP*GP*CP*CP*CP*GP*U)-3'), 1.5 MM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP* REMARK 210 CP*AP*CP*U)-3'), 80 MM SODIUM CHLORIDE, 10 MM SODIUM PHOSPHATE, REMARK 210 0.5 MM EDTA, 90% H2O/10% D2O; 1.5 MM RNA (5'-R(*GP*UP*GP*AP*AP* REMARK 210 GP*CP*CP*CP*GP*U)-3'), 1.5 MM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP* REMARK 210 AP*CP*U)-3'), 80 MM SODIUM CHLORIDE, 10 MM SODIUM PHOSPHATE, 0.5 REMARK 210 MM EDTA-10, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-1H COSY; 2D 31P-1H COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.3, SPARKY 3.114, REMARK 210 AMBER, VNMR 6.1C, CNS 1.2 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : NO RESTRAINT VIOLATIONS; LOW REMARK 210 CONSTRAINT ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 U A 2 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 C A 8 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 C A 9 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 C B 12 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 A B 18 N1 - C6 - N6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 C B 19 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 A B 20 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 C B 21 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 C A 8 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 C A 9 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 C B 12 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 G B 17 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 C B 19 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 C B 21 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 C B 21 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 3 C A 8 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 3 C A 9 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 3 C B 12 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 3 G B 17 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 C B 19 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 3 C B 21 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 C B 21 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 C B 21 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 4 U A 2 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 A A 4 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 C A 8 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 4 C A 9 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 4 C B 12 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 4 G B 17 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 C B 19 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 4 C B 21 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 5 C A 8 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 5 C A 9 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 5 C B 12 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 5 G B 17 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 5 C B 19 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 5 C B 21 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 6 C A 8 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 6 C A 9 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 6 C B 12 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 6 A B 18 N1 - C6 - N6 ANGL. DEV. = -3.8 DEGREES REMARK 500 6 C B 19 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 6 C B 21 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 6 C B 21 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 6 U B 22 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 7 C A 8 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 7 C A 9 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 7 C B 12 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 7 C B 19 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 7 C B 21 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 72 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 2 G B 17 0.10 SIDE CHAIN REMARK 500 3 G A 6 0.05 SIDE CHAIN REMARK 500 3 G B 17 0.09 SIDE CHAIN REMARK 500 3 U B 22 0.07 SIDE CHAIN REMARK 500 4 G B 17 0.10 SIDE CHAIN REMARK 500 5 G A 6 0.06 SIDE CHAIN REMARK 500 5 G B 17 0.10 SIDE CHAIN REMARK 500 6 G B 17 0.07 SIDE CHAIN REMARK 500 6 U B 22 0.07 SIDE CHAIN REMARK 500 7 G B 17 0.07 SIDE CHAIN REMARK 500 7 A B 18 0.06 SIDE CHAIN REMARK 500 8 G A 6 0.05 SIDE CHAIN REMARK 500 8 G B 17 0.09 SIDE CHAIN REMARK 500 9 G B 17 0.07 SIDE CHAIN REMARK 500 10 G B 17 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17406 RELATED DB: BMRB DBREF 2L8F A 1 11 PDB 2L8F 2L8F 1 11 DBREF 2L8F B 12 22 PDB 2L8F 2L8F 12 22 SEQRES 1 A 11 G U G A A G C C C G U SEQRES 1 B 11 C G G A G G A C A C U CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 177 0 0 0 0 0 0 6 0 0 0 2 END